Merge branch 'hotfix-1.29.1'

gemma-cli/pom.xml

@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.0</version>
+ <version>1.29.1</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBioSequenceDetachCli.java

@@ -103,7 +103,6 @@ protected void doWork() throws Exception {
  }
 
 
-
  }
 
  @Override
@@ -114,8 +113,7 @@ public String getShortDesc() {
 
  private void audit( ArrayDesign arrayDesign, String message ) {
  super.getArrayDesignReportService().generateArrayDesignReport( arrayDesign.getId() );
- AuditEventType eventType = ArrayDesignSequenceRemoveEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, message );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignSequenceRemoveEvent.class, message );
  }
 
 }

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBlatCli.java

@@ -66,8 +66,8 @@ protected void buildOptions( Options options ) {
  super.buildOptions( options );
 
  Option blatResultOption = Option.builder( "b" ).hasArg().argName( "PSL file" ).desc(
- "Blat result file in PSL format (if supplied, BLAT will not be run; will not work with settings that indicate "
- + "multiple platforms to run); -t option overrides" )
+  "Blat result file in PSL format (if supplied, BLAT will not be run; will not work with settings that indicate "
+  + "multiple platforms to run); -t option overrides" )
  .longOpt( "blatfile" )
  .build();
 
@@ -80,13 +80,13 @@ protected void buildOptions( Options options ) {
  options.addOption( Option.builder( "sensitive" ).desc( "Run on more sensitive server, if available" ).build() );
 
  Option taxonOption = Option.builder( "t" ).hasArg().argName( "taxon" ).desc(
- "Taxon common name (e.g., human); if platform name not given (analysis will be "
- + "restricted to sequences on that platform for taxon given), blat "
- + "will be run for all ArrayDesigns from that taxon (overrides -a and -b)" )
+  "Taxon common name (e.g., human); if platform name not given (analysis will be "
+  + "restricted to sequences on that platform for taxon given), blat "
+  + "will be run for all ArrayDesigns from that taxon (overrides -a and -b)" )
  .build();
 
  options.addOption( taxonOption );
- // this.addThreadsOption( options );
+  // this.addThreadsOption( options );
  options.addOption( blatScoreThresholdOption );
  options.addOption( blatResultOption );
  }
@@ -143,7 +143,7 @@ protected void doWork() throws Exception {
 
  for ( ArrayDesign arrayDesign : this.getArrayDesignsToProcess() ) {
  if ( !this.shouldRun( skipIfLastRunLaterThan, arrayDesign, ArrayDesignSequenceAnalysisEvent.class ) ) {
- AbstractCLI.log.warn( arrayDesign + " does not meet criteria to be processed");
+ AbstractCLI.log.warn( arrayDesign + " does not meet criteria to be processed" );
  return;
  }
 
@@ -204,8 +204,7 @@ public String getShortDesc() {
 
  private void audit( ArrayDesign arrayDesign, String note ) {
  getArrayDesignReportService().generateArrayDesignReport( arrayDesign.getId() );
- AuditEventType eventType = ArrayDesignSequenceAnalysisEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignSequenceAnalysisEvent.class, note );
  }
 
  /**

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeMapperCli.java

@@ -83,52 +83,52 @@ protected void buildOptions( Options options ) {
  super.buildOptions( options );
 
  options.addOption( Option.builder( "i" ).hasArg().argName( "value" ).desc(
- "Sequence identity threshold, default = " + ProbeMapperConfig.DEFAULT_IDENTITY_THRESHOLD )
+  "Sequence identity threshold, default = " + ProbeMapperConfig.DEFAULT_IDENTITY_THRESHOLD )
  .longOpt( "identityThreshold" ).build() );
 
  options.addOption( Option.builder( "s" ).hasArg().argName( "value" )
  .desc( "Blat score threshold, default = " + ProbeMapperConfig.DEFAULT_SCORE_THRESHOLD )
  .longOpt( "scoreThreshold" ).build() );
 
  options.addOption( Option.builder( "o" ).hasArg().argName( "value" ).desc(
- "Minimum fraction of probe overlap with exons, default = "
- + ProbeMapperConfig.DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION )
+  "Minimum fraction of probe overlap with exons, default = "
+  + ProbeMapperConfig.DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION )
  .longOpt( "overlapThreshold" )
  .build() );
 
  options.addOption( Option.builder( "usePred" ).desc(
- "Allow mapping to predicted genes (overrides Acembly, Ensembl and Nscan; default="
- + ProbeMapperConfig.DEFAULT_ALLOW_PREDICTED + ")" )
+  "Allow mapping to predicted genes (overrides Acembly, Ensembl and Nscan; default="
+  + ProbeMapperConfig.DEFAULT_ALLOW_PREDICTED + ")" )
  .build() );
 
  options.addOption( Option.builder( ArrayDesignProbeMapperCli.CONFIG_OPTION ).hasArg().argName( "configstring" ).desc(
- "String describing which tracks to search, for example 'rkenmias' for all, 'rm' to limit search to Refseq with mRNA evidence. If this option is not set,"
- + " all will be used except as listed below and in combination with the 'usePred' option:\n "
+  "String describing which tracks to search, for example 'rkenmias' for all, 'rm' to limit search to Refseq with mRNA evidence. If this option is not set,"
+  + " all will be used except as listed below and in combination with the 'usePred' option:\n "
 
- + ArrayDesignProbeMapperCli.OPTION_REFSEQ
- + " - search refseq track for genes (best to leave on)\n"
+  + ArrayDesignProbeMapperCli.OPTION_REFSEQ
+  + " - search refseq track for genes (best to leave on)\n"
 
- + ArrayDesignProbeMapperCli.OPTION_KNOWNGENE
- + " - search knownGene track for genes (best to leave on, but track may be missing for some organisms)\n"
+  + ArrayDesignProbeMapperCli.OPTION_KNOWNGENE
+  + " - search knownGene track for genes (best to leave on, but track may be missing for some organisms)\n"
 
- + ArrayDesignProbeMapperCli.OPTION_MICRORNA + " - search miRNA track for genes (Default = false)\n"
+  + ArrayDesignProbeMapperCli.OPTION_MICRORNA + " - search miRNA track for genes (Default = false)\n"
 
- + ArrayDesignProbeMapperCli.OPTION_EST + " - search EST track for transcripts (Default=false)\n"
+  + ArrayDesignProbeMapperCli.OPTION_EST + " - search EST track for transcripts (Default=false)\n"
 
- + ArrayDesignProbeMapperCli.OPTION_MRNA
- + " - search mRNA track for transcripts (Default=false)\n"
+  + ArrayDesignProbeMapperCli.OPTION_MRNA
+  + " - search mRNA track for transcripts (Default=false)\n"
 
- + ArrayDesignProbeMapperCli.OPTION_ENSEMBL + " - search Ensembl track for predicted genes (Default=false) \n" )
+  + ArrayDesignProbeMapperCli.OPTION_ENSEMBL + " - search Ensembl track for predicted genes (Default=false) \n" )
  .build() );
 
  options.addOption( Option.builder( ArrayDesignProbeMapperCli.MIRNA_ONLY_MODE_OPTION ).desc(
- "Only seek miRNAs; this is the same as '-config " + ArrayDesignProbeMapperCli.OPTION_MICRORNA
- + "; overrides -config." )
+  "Only seek miRNAs; this is the same as '-config " + ArrayDesignProbeMapperCli.OPTION_MICRORNA
+  + "; overrides -config." )
  .build() );
 
  Option taxonOption = Option.builder( "t" ).hasArg().argName( "taxon" ).desc(
- "Taxon common name (e.g., human); if using '-import', this taxon will be assumed; otherwise analysis will be run for all"
- + " ArrayDesigns from that taxon (overrides -a)" )
+  "Taxon common name (e.g., human); if using '-import', this taxon will be assumed; otherwise analysis will be run for all"
+  + " ArrayDesigns from that taxon (overrides -a)" )
  .build();
 
  options.addOption( taxonOption );
@@ -138,10 +138,10 @@ protected void buildOptions( Options options ) {
  options.addOption( force );
 
  Option directAnnotation = Option.builder( "import" ).desc(
- "Import annotations from a file rather than our own analysis. You must provide the taxon option. "
- + "File format: 2 columns with column 1= probe name in Gemma, "
- + "column 2=sequence name (not required, and not used for direct gene-based annotation)"
- + " column 3 = gene symbol (will be matched to that in Gemma)" )
+  "Import annotations from a file rather than our own analysis. You must provide the taxon option. "
+  + "File format: 2 columns with column 1= probe name in Gemma, "
+  + "column 2=sequence name (not required, and not used for direct gene-based annotation)"
+  + " column 3 = gene symbol (will be matched to that in Gemma)" )
  .hasArg().argName( "file" )
  .build();
 
@@ -356,7 +356,7 @@ boolean needToRun( Date skipIfLastRunLaterThan, ArrayDesign arrayDesign,
 // return false;
  AbstractCLI.log
  .warn( arrayDesign + ": Sequences were updated more recently than the last repeat masking but requirement temporarily waived" );
- // return false;
+  // return false;
  }
 
  if ( lastSequenceAnalysis != null && lastSequenceUpdate.getDate()
@@ -381,8 +381,8 @@ boolean needToRun( Date skipIfLastRunLaterThan, ArrayDesign arrayDesign,
  if ( isNotMerged && lastRepeatMask == null ) {
  AbstractCLI.log
  .warn( arrayDesign + "Repeat masking missing but requirement temporarily waived" );
- // AbstractCLI.log.warn( arrayDesign + ": Must do repeat mask analysis before probe mapping" );
- // return false;
+  // AbstractCLI.log.warn( arrayDesign + ": Must do repeat mask analysis before probe mapping" );
+  // return false;
  }
 
  if ( skipIfLastRunLaterThan != null && lastProbeMapping != null && lastProbeMapping.getDate()
@@ -440,7 +440,7 @@ protected void doWork() throws Exception {
  }
  arrayDesignProbeMapperService
  .processArrayDesign( arrayDesign, taxon, f, this.sourceDatabase, this.ncbiIds );
- this.audit( arrayDesign, "Imported from " + f, new AnnotationBasedGeneMappingEvent() );
+ this.audit( arrayDesign, "Imported from " + f, AnnotationBasedGeneMappingEvent.class );
  } catch ( IOException e ) {
  addErrorObject( arrayDesign, e.getMessage(), e );
  }
@@ -460,13 +460,13 @@ protected void doWork() throws Exception {
  if ( useDB ) {
 
  if ( this.mirnaOnlyModeOption ) {
- this.audit( arrayDesign, "Run in miRNA-only mode.", new AlignmentBasedGeneMappingEvent() );
+ this.audit( arrayDesign, "Run in miRNA-only mode.", AlignmentBasedGeneMappingEvent.class );
  } else if ( configOption != null ) {
  this.audit( arrayDesign, "Run with configuration=" + this.configOption,
- new AlignmentBasedGeneMappingEvent() );
+ AlignmentBasedGeneMappingEvent.class );
  } else {
  this.audit( arrayDesign, "Run with default parameters",
- new AlignmentBasedGeneMappingEvent() );
+ AlignmentBasedGeneMappingEvent.class );
  }
  updateMergedOrSubsumed( arrayDesign );
  }
@@ -497,7 +497,7 @@ public String getShortDesc() {
  return "Process the BLAT results for an array design to map them onto genes";
  }
 
- private void audit( ArrayDesign arrayDesign, String note, ArrayDesignGeneMappingEvent eventType ) {
+ private void audit( ArrayDesign arrayDesign, String note, Class<? extends ArrayDesignGeneMappingEvent> eventType ) {
  getArrayDesignReportService().generateArrayDesignReport( arrayDesign.getId() );
  auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
  }
@@ -527,7 +527,7 @@ private void configure( ArrayDesign arrayDesign ) {
  * Hackery to work around rn6+ problems
  */
  boolean isRat;
- if ( this.taxon == null) {
+ if ( this.taxon == null ) {
  assert arrayDesign != null;
  Taxon t = getArrayDesignService().getTaxon( arrayDesign.getId() );
  isRat = t.getCommonName().equals( "rat" );
@@ -614,8 +614,7 @@ private void processArrayDesign( Date skipIfLastRunLaterThan, ArrayDesign design
  }
  arrayDesignProbeMapperService.processArrayDesign( design, this.config, this.useDB );
  addSuccessObject( design, "Successfully processed " + design );
- ArrayDesignGeneMappingEvent eventType = new AlignmentBasedGeneMappingEvent();
- this.audit( design, "Part of a batch job", eventType );
+ this.audit( design, "Part of a batch job", AlignmentBasedGeneMappingEvent.class );
 
  updateMergedOrSubsumed( design );
 
@@ -638,7 +637,7 @@ private void updateMergedOrSubsumed( ArrayDesign design ) {
  Collection<ArrayDesign> toUpdate = getRelatedDesigns( design );
  for ( ArrayDesign ad : toUpdate ) {
  log.info( "Marking subsumed or merged design as completed, updating report: " + ad );
- this.audit( ad, "Parent design was processed (merged or subsumed by this)", AlignmentBasedGeneMappingEvent.Factory.newInstance() );
+ this.audit( ad, "Parent design was processed (merged or subsumed by this)", AlignmentBasedGeneMappingEvent.class );
  arrayDesignProbeMapperService.deleteOldFiles( ad );
  getArrayDesignReportService().generateArrayDesignReport( ad.getId() );
  }

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeRenamerCli.java

@@ -139,8 +139,7 @@ private void rename( ArrayDesign arrayDesign, InputStream newIdFile ) {
 
  private void audit( ArrayDesign arrayDesign, String note ) {
  super.getArrayDesignReportService().generateArrayDesignReport( arrayDesign.getId() );
- AuditEventType eventType = ArrayDesignProbeRenamingEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignProbeRenamingEvent.class, note );
  }
 
  private Map<String, String> parseIdFile( InputStream newIdFile ) throws IOException {

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignRepeatScanCli.java

@@ -130,8 +130,7 @@ public String getShortDesc() {
  }
 
  private void audit( ArrayDesign arrayDesign, String note ) {
- AuditEventType eventType = ArrayDesignRepeatAnalysisEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignRepeatAnalysisEvent.class, note );
  }
 
  private void processArrayDesign( ArrayDesign design ) {

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignSequenceAssociationCli.java

@@ -257,8 +257,7 @@ protected void processOptions( CommandLine commandLine ) {
  private void audit( ArrayDesign arrayDesign, String note ) {
  // minor : don't add audit event if no sequences were changed, or --force.
  this.getArrayDesignReportService().generateArrayDesignReport( arrayDesign.getId() );
- AuditEventType eventType = ArrayDesignSequenceUpdateEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignSequenceUpdateEvent.class, note );
  }
 
 }

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignSubsumptionTesterCli.java

@@ -152,8 +152,7 @@ protected void processOptions( CommandLine commandLine ) {
  }
 
  private void audit( ArrayDesign arrayDesign, String note ) {
- AuditEventType eventType = ArrayDesignSubsumeCheckEvent.Factory.newInstance();
- auditTrailService.addUpdateEvent( arrayDesign, eventType, note );
+ auditTrailService.addUpdateEvent( arrayDesign, ArrayDesignSubsumeCheckEvent.class, note );
  }
 
 }

gemma-cli/src/main/java/ubic/gemma/core/apps/ExpressionDataCorrMatCli.java

@@ -67,7 +67,7 @@ protected void buildOptions( Options options ) {
  }
 
  private void audit( ExpressionExperiment ee ) {
- auditTrailService.addUpdateEvent( ee, null, "Generated sample correlation matrix" );
+ auditTrailService.addUpdateEvent( ee, "Generated sample correlation matrix" );
  addSuccessObject( ee, "Successfully processed " + ee.getShortName() );
  }
 

gemma-cli/src/main/java/ubic/gemma/core/apps/ExpressionExperimentDataFileGeneratorCli.java

@@ -116,12 +116,11 @@ private void processExperiment( ExpressionExperiment ee ) {
  ee = this.eeService.thawLite( ee );
 
  AuditTrailService ats = this.getBean( AuditTrailService.class );
- AuditEventType type = CommentedEvent.Factory.newInstance();
 
  expressionDataFileService.writeOrLocateCoexpressionDataFile( ee, force_write );
  expressionDataFileService.writeOrLocateDiffExpressionDataFiles( ee, force_write );
 
- ats.addUpdateEvent( ee, type, "Generated Flat data files for downloading" );
+ ats.addUpdateEvent( ee, CommentedEvent.class, "Generated Flat data files for downloading" );
  addSuccessObject( ee, "Success: generated data file for " + ee.getShortName() + " ID=" + ee.getId() );
 
  } catch ( Exception e ) {